#include <ctype.h>
#include "bam.h"
#include "khash.h"
-KHASH_MAP_INIT_INT(aux, uint8_t*)
KHASH_MAP_INIT_STR(s, int)
+void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
+{
+ int ori_len = b->data_len;
+ b->data_len += 3 + len;
+ b->l_aux += 3 + len;
+ if (b->m_data < b->data_len) {
+ b->m_data = b->data_len;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
+ b->data[ori_len + 2] = type;
+ memcpy(b->data + ori_len + 3, data, len);
+}
+
+uint8_t *bam_aux_get(bam1_t *b, const char tag[2])
+{
+ uint8_t *s;
+ int y = tag[0]<<8 | tag[1];
+ s = bam1_aux(b);
+ while (s < b->data + b->data_len) {
+ int type, x = (int)s[0]<<8 | s[1];
+ s += 2;
+ if (x == y) return s;
+ type = toupper(*s); ++s;
+ if (type == 'C') ++s;
+ else if (type == 'S') s += 2;
+ else if (type == 'I' || type == 'F') s += 4;
+ else if (type == 'D') s += 8;
+ else if (type == 'Z' || type == 'H') { while (*s) putchar(*s++); ++s; }
+ }
+ return 0;
+}
+
void bam_init_header_hash(bam_header_t *header)
{
if (header->hash == 0) {
bam_init_header_hash(header);
h = (khash_t(s)*)header->hash;
-
+
l = strlen(str);
p = s = (char*)malloc(l+1);
/* squeeze out "," */
free(s);
}
-void bam_aux_init(bam1_t *b)
-{
- khash_t(aux) *h;
- uint8_t *s;
- if (b->hash == 0) {
- h = kh_init(aux);
- b->hash = h;
- } else {
- h = (khash_t(aux)*)b->hash;
- kh_clear(aux, h);
- }
- s = bam1_aux(b);
- while (s < b->data + b->data_len) {
- uint32_t x = (uint32_t)s[0]<<8 | s[1];
- int ret, type;
- khint_t k;
- s += 2; type = toupper(*s); ++s;
- k = kh_put(aux, h, x, &ret);
- kh_value(h, k) = s;
- if (type == 'C') ++s;
- else if (type == 'S') s += 2;
- else if (type == 'I') s += 4;
- else if (type == 'F') s += 4;
- else if (type == 'Z') { while (*s) putchar(*s++); ++s; }
- }
-}
-void bam_aux_destroy(bam1_t *b)
-{
- khash_t(aux) *h = (khash_t(aux)*)b->hash;
- kh_destroy(aux, h);
- b->hash = 0;
-}
-static uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
-{
- uint32_t x = (uint32_t)tag[0]<<8 | tag[1];
- khint_t k;
- khash_t(aux) *h;
- if (b->hash == 0) bam_aux_init(b);
- h = (khash_t(aux)*)b->hash;
- k = kh_get(aux, h, x);
- if (k == kh_end(h)) return 0;
- return kh_value(h, k);
-}
-int32_t bam_aux_geti(bam1_t *b, const char tag[2], int *err)
+int32_t bam_aux2i(const uint8_t *s)
{
int type;
- uint8_t *s = bam_aux_get_core(b, tag);
- *err = 0;
- if (s == 0) { *err = -1; return 0; }
+ if (s == 0) return 0;
type = *s++;
if (type == 'c') return (int32_t)*(int8_t*)s;
else if (type == 'C') return (int32_t)*(uint8_t*)s;
else if (type == 's') return (int32_t)*(int16_t*)s;
else if (type == 'S') return (int32_t)*(uint16_t*)s;
else if (type == 'i' || type == 'I') return *(int32_t*)s;
- else { *err = -2; return 0; }
+ else return 0;
}
-float bam_aux_getf(bam1_t *b, const char tag[2], int *err)
+
+float bam_aux2f(const uint8_t *s)
{
int type;
- uint8_t *s = bam_aux_get_core(b, tag);
- *err = 0;
type = *s++;
- if (s == 0) { *err = -1; return 0; }
+ if (s == 0) return 0.0;
if (type == 'f') return *(float*)s;
- else { *err = -2; return 0; }
+ else return 0.0;
+}
+
+double bam_aux2d(const uint8_t *s)
+{
+ int type;
+ type = *s++;
+ if (s == 0) return 0.0;
+ if (type == 'd') return *(double*)s;
+ else return 0.0;
}
-char bam_aux_getc(bam1_t *b, const char tag[2], int *err)
+
+char bam_aux2A(const uint8_t *s)
{
int type;
- uint8_t *s = bam_aux_get_core(b, tag);
- *err = 0;
type = *s++;
- if (s == 0) { *err = -1; return 0; }
- if (type == 'c') return *(char*)s;
- else { *err = -2; return 0; }
+ if (s == 0) return 0;
+ if (type == 'A') return *(char*)s;
+ else return 0;
}
-char *bam_aux_getZH(bam1_t *b, const char tag[2], int *err)
+
+char *bam_aux2Z(const uint8_t *s)
{
int type;
- uint8_t *s = bam_aux_get_core(b, tag);
- *err = 0;
type = *s++;
- if (s == 0) { *err = -1; return 0; }
+ if (s == 0) return 0;
if (type == 'Z' || type == 'H') return (char*)s;
- else { *err = -2; return 0; }
+ else return 0;
+}
+
+char bam_aux_getCSi(bam1_t *b, int i)
+{
+ uint8_t *c = bam_aux_get(b, "CS");
+ char *cs = NULL;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cs = bam_aux2Z(c);
+ // adjust for strandedness and leading adaptor
+ if(bam1_strand(b)) i = strlen(cs) - 1 - i;
+ else i++;
+ return cs[i];
+}
+
+char bam_aux_getCQi(bam1_t *b, int i)
+{
+ uint8_t *c = bam_aux_get(b, "CQ");
+ char *cq = NULL;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cq = bam_aux2Z(c);
+ // adjust for strandedness
+ if(bam1_strand(b)) i = strlen(cq) - 1 - i;
+ return cq[i];
+}
+
+char bam_aux_nt2int(char a)
+{
+ switch(toupper(a)) {
+ case 'A':
+ return 0;
+ break;
+ case 'C':
+ return 1;
+ break;
+ case 'G':
+ return 2;
+ break;
+ case 'T':
+ return 3;
+ break;
+ default:
+ return 4;
+ break;
+ }
+}
+
+char bam_aux_ntnt2cs(char a, char b)
+{
+ a = bam_aux_nt2int(a);
+ b = bam_aux_nt2int(b);
+ if(4 == a || 4 == b) return '4';
+ return "0123"[(int)(a ^ b)];
+}
+
+char bam_aux_getCEi(bam1_t *b, int i)
+{
+ int cs_i;
+ uint8_t *c = bam_aux_get(b, "CS");
+ char *cs = NULL;
+ char prev_b, cur_b;
+ char cur_color, cor_color;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cs = bam_aux2Z(c);
+
+ // adjust for strandedness and leading adaptor
+ if(bam1_strand(b)) { //reverse strand
+ cs_i = strlen(cs) - 1 - i;
+ // get current color
+ cur_color = cs[cs_i];
+ // get previous base
+ prev_b = (0 == cs_i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
+ // get current base
+ cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
+ }
+ else {
+ cs_i=i+1;
+ // get current color
+ cur_color = cs[cs_i];
+ // get previous base
+ prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)];
+ // get current base
+ cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
+ }
+
+ // corrected color
+ cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
+
+ if(cur_color == cor_color) {
+ return '-';
+ }
+ else {
+ return cur_color;
+ }
}
projects / samtools.git / blobdiff